!*****************************************************************************
! Example file XDS.INP for the MAR345 and MAR555 (X-ray Research).
! Characters in a line to the right of an exclamation mark are comment.
!*****************************************************************************
 DETECTOR=MAR345  MINIMUM_VALID_PIXEL_VALUE=0  OVERLOAD=130000
 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 ! 0.0 cos(2theta) sin(2theta)
 TRUSTED_REGION=0.0 0.99 !Relative radii limiting trusted detector region
 ORGX=1249.71 ORGY=1255.47  !Detector origin (pixels).  ORGX=NX/2; ORGY=NY/2
!UNTRUSTED_RECTANGLE= 570 1920  1469 2048  ! rectangle: X1 X2   Y1 Y2
!UNTRUSTED_ELLIPSE=1150 1350    1150 1350  ! ellipse enclosed by X1 X2 Y1 Y2
!UNTRUSTED_QUADRILATERAL=565 574  1519 1552  1508 1533  566 1536
 ROFF=0.0 TOFF=0.0!Radial & tangential offset for spiral read-out scanners
!File name, access, format of dark-current (non-Xray background) image
!DARK_CURRENT_IMAGE=../images/blank.tif    !hardly ever used

!MAXIMUM_NUMBER_OF_JOBS=4  !Speeds-up COLSPOT & INTEGRATE on a Linux-cluster
!MAXIMUM_NUMBER_OF_PROCESSORS=4!<33;ignored by single cpu version of xds
!SECONDS=0   !Maximum number of seconds to wait until data image must appear
!TEST=1     !Test flag. 1,2 additional diagnostics and images

!NX=number of fast pixels (along X); QX=length of an X-pixel (mm)
!NY=number of slow pixels (along Y); QY=length of a  Y-pixel (mm)
!For the MAR345 and MAR555, the number of detector pixels and their sizes 
!are obtained from the image header. It is therefore unnecessary to
!specify values for NX, NY, QX, QY.
!NX=1200 NY=1200 QX=0.15 QY=0.15  !images  ???.mar1200 or ???.pck1200
!NX=1600 NY=1600 QX=0.15 QY=0.15  !images  ???.mar1600 or ???.pck1600
!NX=2000 NY=2000 QX=0.15 QY=0.15  !images  ???.mar2000 or ???.pck2000
!NX=2300 NY=2300 QX=0.15 QY=0.15  !images  ???.mar2300 or ???.pck2300
!NX=1800 NY=1800 QX=0.10 QY=0.10  !images  ???.mar1800 or ???.pck1800
!NX=2400 NY=2400 QX=0.10 QY=0.10  !images  ???.mar2400 or ???.pck2400
!NX=3000 NY=3000 QX=0.10 QY=0.10  !images  ???.mar3000 or ???.pck3000
!NX=3450 NY=3450 QX=0.10 QY=0.10  !images  ???.mar3450 or ???.pck3450
!NX=2560 NY=3072 QX=0.139 QY=0.139!for MAR555 images

!AIR=0.001 !Air absorption coefficient of x-rays is computed by XDS by default

!====================== JOB CONTROL PARAMETERS ===============================
!JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT

!====================== GEOMETRICAL PARAMETERS ===============================
!ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2
 ORGX=1249.71 ORGY=1255.47  !Detector origin (pixels).  ORGX=NX/2; ORGY=NY/2
 DETECTOR_DISTANCE= 101.4   !(mm)

 ROTATION_AXIS= 1.0 0.0 0.0
 OSCILLATION_RANGE=1.0            !degrees (>0)

 X-RAY_WAVELENGTH=1.5418          !Angstroem
 INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
!FRACTION_OF_POLARIZATION=0.90 !default=0.5 for unpolarized beam
 POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0

!======================= CRYSTAL PARAMETERS =================================
!SPACE_GROUP_NUMBER=96   !0 for unknown crystals; cell constants are ignored.
 UNIT_CELL_CONSTANTS= 79.092 79.092 38.076  90 90 90

! You may specify here the x,y,z components for the unit cell vectors if
! known from a previous run using the same crystal in the same orientation
!UNIT_CELL_A-AXIS=
!UNIT_CELL_B-AXIS=
!UNIT_CELL_C-AXIS=

!Optional reindexing transformation to apply on reflection indices
!REIDX=   0  0 -1  0  0 -1  0  0 -1  0  0  0

!FRIEDEL'S_LAW=FALSE !Default is TRUE.

!==================== SELECTION OF DATA IMAGES ==============================
!Generic file name and format (optional) of data images
 NAME_TEMPLATE_OF_DATA_FRAMES=../images/CoA4b_???.mar2300  ! MAR345

 DATA_RANGE=1 19       !Numbers of first and last data image collected

 BACKGROUND_RANGE=1 5  !Numbers of first and last data image for background

!SPOT_RANGE=1 19       !First and last data image number for finding spots

!==================== DATA COLLECTION STRATEGY (XPLAN) ======================
!                       !!! Warning !!!
! If you processed your data for a crystal with unknown cell constants and
! space group symmetry, XPLAN will report the results for space group P1.

!STARTING_ANGLE=  0.0      STARTING_FRAME=1
!used to define the angular origin about the rotation axis.
!Default:  STARTING_ANGLE=  0 at STARTING_FRAME=first data image

!RESOLUTION_SHELLS=10 6 5 4 3 2 1.5 1.3 1.2

!STARTING_ANGLES_OF_SPINDLE_ROTATION= 0 180 10

!TOTAL_SPINDLE_ROTATION_RANGES=30.0 120 15

!REFERENCE_DATA_SET= CK.HKL   !Name of a reference data set (optional)

!====================== INDEXING PARAMETERS =================================
!Never forget to check this, since the default 0 0 0 is almost always correct!
!INDEX_ORIGIN= 0 0 0          ! used by "IDXREF" to add an index offset

!Additional parameters for fine tuning that rarely need to be changed
!INDEX_ERROR=0.05 INDEX_MAGNITUDE=8 INDEX_QUALITY=0.8
!SEPMIN=6.0 CLUSTER_RADIUS=3
!MAXIMUM_ERROR_OF_SPOT_POSITION=3.0
!MAXIMUM_ERROR_OF_SPINDLE_POSITION=2.0
!MINIMUM_FRACTION_OF_INDEXED_SPOTS=0.5

!============== DECISION CONSTANTS FOR FINDING CRYSTAL SYMMETRY =============
!Decision constants for detection of lattice symmetry (IDXREF, CORRECT)
 MAX_CELL_AXIS_ERROR=0.03 ! Maximum relative error in cell axes tolerated
 MAX_CELL_ANGLE_ERROR=2.0 ! Maximum cell angle error tolerated

!Decision constants for detection of space group symmetry (CORRECT).
!Resolution range for accepting reflections for space group determination in
!the CORRECT step. It should cover a sufficient number of strong reflections.
 TEST_RESOLUTION_RANGE=8.0 4.5
 MIN_RFL_Rmeas= 50 ! Minimum #reflections needed for calculation of Rmeas
 MAX_FAC_Rmeas=2.0 ! Sets an upper limit for acceptable Rmeas

!================= PARAMETERS CONTROLLING REFINEMENTS =======================
!REFINE(IDXREF)=BEAM AXIS ORIENTATION CELL !DISTANCE
!REFINE(INTEGRATE)=!DISTANCE BEAM ORIENTATION CELL !AXIS
!REFINE(CORRECT)=DISTANCE BEAM ORIENTATION CELL AXIS

!================== CRITERIA FOR ACCEPTING REFLECTIONS ======================
 VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000 !Used by DEFPIX
				   !for excluding shaded parts of the detector.

 INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT

!used by CORRECT to exclude ice-reflections
!EXCLUDE_RESOLUTION_RANGE= 3.93 3.87 !ice-ring at 3.897 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 3.70 3.64 !ice-ring at 3.669 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 3.47 3.41 !ice-ring at 3.441 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 2.70 2.64 !ice-ring at 2.671 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 2.28 2.22 !ice-ring at 2.249 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 2.102 2.042 !ice-ring at 2.072 Angstrom - strong
!EXCLUDE_RESOLUTION_RANGE= 1.978 1.918 !ice-ring at 1.948 Angstrom - weak
!EXCLUDE_RESOLUTION_RANGE= 1.948 1.888 !ice-ring at 1.918 Angstrom - strong
!EXCLUDE_RESOLUTION_RANGE= 1.913 1.853 !ice-ring at 1.883 Angstrom - weak
!EXCLUDE_RESOLUTION_RANGE= 1.751 1.691 !ice-ring at 1.721 Angstrom - weak

!MINIMUM_ZETA=0.05 !Defines width of 'blind region' (XPLAN,INTEGRATE,CORRECT)

!WFAC1=1.0  !This controls the number of rejected MISFITS in CORRECT;
	    !a larger value leads to fewer rejections.
!REJECT_ALIEN=20.0 ! Automatic rejection of very strong reflections

!============== INTEGRATION AND PEAK PROFILE PARAMETERS =====================
!Specification of the peak profile parameters below overrides the automatic
!determination from the images
!Suggested values are listed near the end of INTEGRATE.LP
!BEAM_DIVERGENCE=   0.80         !arctan(spot diameter/DETECTOR_DISTANCE)
!BEAM_DIVERGENCE_E.S.D.=   0.080 !half-width (Sigma) of BEAM_DIVERGENCE
!REFLECTING_RANGE=  0.780 !for crossing the Ewald sphere on shortest route
!REFLECTING_RANGE_E.S.D.=  0.113 !half-width (mosaicity) of REFLECTING_RANGE

!NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=9 !used by: INTEGRATE
!NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA= 9     !used by: INTEGRATE

!CUT=2.0    !defines the integration region for profile fitting
!MINPK=75.0 !minimum required percentage of observed reflection intensity
!DELPHI= 5.0!controls the number of reference profiles and scaling factors

!======= PARAMETERS CONTROLLING CORRECTION FACTORS (used by: CORRECT) =======
!MINIMUM_I/SIGMA=3.0 !minimum intensity/sigma required for scaling reflections
!NBATCH=-1  !controls the number of correction factors along image numbers
!REFLECTIONS/CORRECTION_FACTOR=50   !minimum #reflections/correction needed
!PATCH_SHUTTER_PROBLEM=TRUE         !FALSE is default
!STRICT_ABSORPTION_CORRECTION=TRUE  !FALSE is default
!CORRECTIONS= DECAY MODULATION ABSORPTION

!=========== PARAMETERS DEFINING BACKGROUND AND PEAK PIXELS =================
!STRONG_PIXEL=3.0                              !used by: COLSPOT
!A 'strong' pixel to be included in a spot must exceed the background
!by more than the given multiple of standard deviations.

!MAXIMUM_NUMBER_OF_STRONG_PIXELS=1500000       !used by: COLSPOT

!SPOT_MAXIMUM-CENTROID=3.0                     !used by: COLSPOT

!MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=6          !used by: COLSPOT
!This allows to suppress spurious isolated pixels from entering the
!spot list generated by "COLSPOT".

!NBX=3  NBY=3  !Define a rectangle of size (2*NBX+1)*(2*NBY+1)
!The variation of counts within the rectangle centered at each image pixel
!is used for distinguishing between background and spot pixels.

!BACKGROUND_PIXEL=6.0                          !used by: COLSPOT,INTEGRATE
!An image pixel does not belong to the background region if the local
!pixel variation exceeds the expected variation by the given number of
!standard deviations.

!SIGNAL_PIXEL=3.0                              !used by: INTEGRATE
!A pixel above the threshold contributes to the spot centroid